2) COver did give a benefit, but remember that your "aiming" was a guideline, not a shooter style. There was a little gauge. Linkers and some other big stuff did go right through total cover sometimes for me, but otherwise total cover worked fine and partial cover was helpful, I think.
1,3,4: These are just elements of MMOs. You want color options (though camo-pattern dies would make perfect sense. A sci-fi game featuring radar on a personal level makes camo redundant), and you want it easy to load and process on a wide variety of computers.
The respawning is something that bugs me on MMO's. It's irksome in the extreme on many games. TR at least has new enemies appear somewhat "in character" such as a drop ship dropping off new troops, or whatnot. They also varied the timing somewhat, which sometimes meant you'd barely killed the guy when he'd be replaced.
More instances are always fun, though I wouldn't want to require groups too much, some of us like to solo.Guild Wars is all instance for example, except for the city safe zones. It's fine by itself, but it pulls away from the MMO flavor of having strangers running by. I'm not sure that instances would feel more "warlike" for me though, pouring troops into a battlefield makes sense.
I do dislike the death-penalty. It feels excessive in a respawning game. In GW, the death penalty is offset by the fact your enemies don't reappear, but in TR, they'll probably reappear before you even get back there, let alone reset the death penalty.
All games have something, but 20% loss to stats is too harsh IMO.
The other thing I always hate in these games is the swarm tactics. Especially when you're running somewhere to get back to a mission and suddenly you've got to handle a swarm of freaking bats. It's terribly unfun.